A trajectory planning process receives data generated by high-level control software. This data defines positions and scan velocities. The trajectory planning process creates sequences of constant acceleration intervals that allow critical motions to be executed at maximum throughput. The trajectory planning process outputs a profile. A profile executor, using the profile output by the trajectory planner process, generates continuous synchronized, filtered, multi-axis position and acceleration commands that drive control servos. Time intervals generated by the trajectory planner are quantized to be integer multiples of a real time clock period. The trajectory planner outputs have infinite jerk, but are smoothed by filters in the profile executor to both limit jerk and minimize servo-tracking errors. The trajectory planner allows time for the profile executor filters, but does not restrict fine tuning of the shape of these filters, provided that the width of the tuned filter does not exceed the allowed time.